Plant Circular RNA Database

Detail information of Zm00001d053515_circ_g.4

			
						 General Information
					
						CircRNA Name
						Zm00001d053515_circ_g.4
					
						ID in PlantcircBase
						zma_circ_008281
					
						Alias
						zma_circ_0001711, GRMZM2G007854_C2
					
						Organism
						
							Zea mays						
					
						Position
						
							chr4: 232717987-232719475  JBrowse»						
					
						Reference genome
						
							AGPv4.38						
					
						Type  
						
							u-circRNA							
									
						Identification method
						find_circ, CIRI2
					
						Parent gene
						
							Zm00001d053515						
					
						Parent gene annotation
						
							Protein kinase superfamily protein
							
						Parent gene strand
						-
					
						Alternative splicing
						
							NA						
					
						Support reads
						NA
					
						Tissues
						leaf, root
					
						Exon boundary  
						
							Yes-Yes							"Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.

						Splicing signals  
						
							CT-AC							The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.

						Number of exons covered
						Zm00001d053515_T014:4
Zm00001d053515_T004:4
Zm00001d053515_T003:4
Zm00001d053515_T008:4
Zm00001d053515_T016:4
Zm00001d053515_T015:4
Zm00001d053515_T013:4
Zm00001d053515_T012:4
Zm00001d053515_T007:4
Zm00001d053515_T009:4
Zm00001d053515_T006:4
Zm00001d053515_T005:4
Zm00001d053515_T002:4

General Information
CircRNA Name	Zm00001d053515_circ_g.4
ID in PlantcircBase	zma_circ_008281
Alias	zma_circ_0001711, GRMZM2G007854_C2
Organism	Zea mays
Position	chr4: 232717987-232719475 JBrowse»
Reference genome	AGPv4.38
Type	u-circRNA
Identification method	find_circ, CIRI2
Parent gene	Zm00001d053515
Parent gene annotation	Protein kinase superfamily protein
Parent gene strand	-
Alternative splicing	NA
Support reads	NA
Tissues	leaf, root
Exon boundary	Yes-Yes "Exon boundary" shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.
Splicing signals	CT-AC The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.
Number of exons covered	Zm00001d053515_T014:4 Zm00001d053515_T004:4 Zm00001d053515_T003:4 Zm00001d053515_T008:4 Zm00001d053515_T016:4 Zm00001d053515_T015:4 Zm00001d053515_T013:4 Zm00001d053515_T012:4 Zm00001d053515_T007:4 Zm00001d053515_T009:4 Zm00001d053515_T006:4 Zm00001d053515_T005:4 Zm00001d053515_T002:4

			
						 Experimental Information
					
						Sanger sequencing for BSS  
						
							NA							Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".

						PCR primers for BSS   
						
							NA							PCR primers used in back-splicing site (BSS) validation.

						Sanger sequencing for FL   
						
							NA							Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.

						PCR primers for FL   
						
							NA							 PCR primers used in full-length (FL) sequence validation.

Experimental Information
Sanger sequencing for BSS	NA Sanger sequencing for back-splicing site (BSS) validation. "Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".
PCR primers for BSS	NA PCR primers used in back-splicing site (BSS) validation.
Sanger sequencing for FL	NA Sanger sequencing for full-length (FL) sequence validation of circRNAs. "Yes" represents Sanger sequencing has been performed to valid the full-length of circRNA, "No" represents the opposite.
PCR primers for FL	NA PCR primers used in full-length (FL) sequence validation.

			
				
						 Sequences
					

				
						Splice junction sequence  
						
							TCCAAAATATGGTGAAATAGAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACG
TTTAAATGAACAAGGAAACAGATTGAACATATTATCctttgagcacatagaggactatttggtt
caagaggagaatcacaggaatcatagtcggctgaatcactttctccagttgcagacatatggga
tgtgacaa

									
								

					

						Assembled circRNA sequence  
						
							Yes
The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).

					

						Full-length trsnacripts
						
							Transcript length: 979
Transcript exons: 232717987-232718225,232718328-232718519,232718832-232719
035,232719132-232719475
CTTTGAGCACATAGAGGACTATTTGGTTCAAGAGGAGAATCACAGGAATCATAGTCGGCTGAAT
CACTTTCTCCAGTTGCAGACATATGGGATGTGACAACAGCTTTGGATGAAAATGGAACTAGTTG
TCCTGGAAAACGCATCAGGTCAACTAGAAACTCCGCAGATTTCAGAATGACCACAACAGACATA
TGTTTGGATGAATTATCATATCCATGAGGTTCTTCATTTGGAATGCCCACCAGCAGTTTAGAAT
CTATACCAACTGAGTCAGCAAGGACTTTAAATAATATAGCTTTGGGCCTGCAAGATCCATGTCT
TATCTGTCCCAGCAATTGAACTCCTCGATTTTCTAATAAATTGGAAAGATCTTCAGAGGATGTT
CTTGCAGGACTGAGATGTGGGTTTGGTCGGTTGTAGAAGTCAAAAACCAAACCTGCAATTTTTT
TTATCATTGCAGCAGGATTTGAATTCAATCCTTTTACCAGTGCTGTGCATAACTGCTTTAAAGC
AGATAGCTTTTTATCTCTTTCTATGTCCACAAGGATAATCTCAGCCTTAAATCCTTCTATTCCA
AGAGAATAAAGGTCATCAGGAGAAGGTATGGTATCAAAATGCTCCTTGAGTCTCTTTTCCGGAA
TAATGGAATAAAAACCATTGGGTATTGGACCTGAAAGGGATCCGCTAGACCATAATGTCTGAGC
AGCCTGCAATGAATGACCAACTTCCCTAGAATCAAGGGAAGAATATGCAGAATCAAAATTCCTT
TCCTGTTTAGTCAGGGGCAGGGACTGGAACTTCTGCTCCAAATGGGAGGGCCAATTCCGGTCTG
AAGGGTGTGTCTGGGATCTTCCTTCATCTCCTGGCAGATCATCCATCTCCAAAATATGGTGAAA
TAGAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACGTTTAAATGAACAAGGAA
ACAGATTGAACATATTATC
						
					

						Genomic sequence
						
							CTTTGAGCACATAGAGGACTATTTGGTTCAAGAGGAGAATCACAGGAATCATAGTCGGCTGAAT
CACTTTCTCCAGTTGCAGACATATGGGATGTGACAACAGCTTTGGATGAAAATGGAACTAGTTG
TCCTGGAAAACGCATCAGGTCAACTAGAAACTCCGCAGATTTCAGAATGACCACAACAGACATA
TGTTTGGATGAATTATCATATCCATGAGGTTCTTCATTTGGAATGCCCTGCACAAGTTATTGAT
GTAGGAAGTAGGATTAGGAAATTCCATTTGAAGAGATGAATACTATTTCATGTTCAGACATACT
GATGAAAGGTAAAAAACATACCACCAGCAGTTTAGAATCTATACCAACTGAGTCAGCAAGGACT
TTAAATAATATAGCTTTGGGCCTGCAAGATCCATGTCTTATCTGTCCCAGCAATTGAACTCCTC
GATTTTCTAATAAATTGGAAAGATCTTCAGAGGATGTTCTTGCAGGACTGAGATGTGGGTTTGG
TCGGTTGTAGAAGTCAAAAACCTGAAATTATCATTAAAAATATGAAGTTAAAGAGAAGTAATAC
ATACTTAATATGGCATTTTATATAGGTCAAAAGAATGAAAAAATAATCAATGGTTTGGAAAGAC
GAAAGATCATTGATACTTCAAGCACCAAGATTACAAATCACCAAATACATGAGCGAAGTAGAAA
TGGAACAGTTTCAACTAGGAAAATTCTATTTAAACCATTTTAAGGTAATCAATCACAAGGGTGA
ATCTTGCAGCACTCTGAAAAGGGAAAAAGTTAGCATGATCATCCTACATTTTGTAAAGAAGCCC
ACGGAAAACTTACCAAACCTGCAATTTTTTTTATCATTGCAGCAGGATTTGAATTCAATCCTTT
TACCAGTGCTGTGCATAACTGCTTTAAAGCAGATAGCTTTTTATCTCTTTCTATGTCCACAAGG
ATAATCTCAGCCTTAAATCCTTCTATTCCAAGAGAATAAAGGTCATCAGGAGAAGGTATGGTAT
CAAAATGCTCCTTGAGTCTCTTTTCCTGCAATGTTCAGAGTCAACAGATGAACTAAAATGCCAA
AGCAAGTTACTCATAATCTTTTAACAAGTTAATGTCATTTAAAAAGGCTTCTCATACCGGAATA
ATGGAATAAAAACCATTGGGTATTGGACCTGAAAGGGATCCGCTAGACCATAATGTCTGAGCAG
CCTGCAATGAATGACCAACTTCCCTAGAATCAAGGGAAGAATATGCAGAATCAAAATTCCTTTC
CTGTTTAGTCAGGGGCAGGGACTGGAACTTCTGCTCCAAATGGGAGGGCCAATTCCGGTCTGAA
GGGTGTGTCTGGGATCTTCCTTCATCTCCTGGCAGATCATCCATCTCCAAAATATGGTGAAATA
GAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACGTTTAAATGAACAAGGAAAC
AGATTGAACATATTATC
						
					

			
		

Sequences
Splice junction sequence	TCCAAAATATGGTGAAATAGAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACG TTTAAATGAACAAGGAAACAGATTGAACATATTATCctttgagcacatagaggactatttggtt caagaggagaatcacaggaatcatagtcggctgaatcactttctccagttgcagacatatggga tgtgacaa
Assembled circRNA sequence	Yes The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or CIRI-full (Zheng and Zhao, 2018) or CIRCexplorer2 (Zhang et al., 2016).
Full-length trsnacripts	Transcript length: 979 Transcript exons: 232717987-232718225,232718328-232718519,232718832-232719 035,232719132-232719475 CTTTGAGCACATAGAGGACTATTTGGTTCAAGAGGAGAATCACAGGAATCATAGTCGGCTGAAT CACTTTCTCCAGTTGCAGACATATGGGATGTGACAACAGCTTTGGATGAAAATGGAACTAGTTG TCCTGGAAAACGCATCAGGTCAACTAGAAACTCCGCAGATTTCAGAATGACCACAACAGACATA TGTTTGGATGAATTATCATATCCATGAGGTTCTTCATTTGGAATGCCCACCAGCAGTTTAGAAT CTATACCAACTGAGTCAGCAAGGACTTTAAATAATATAGCTTTGGGCCTGCAAGATCCATGTCT TATCTGTCCCAGCAATTGAACTCCTCGATTTTCTAATAAATTGGAAAGATCTTCAGAGGATGTT CTTGCAGGACTGAGATGTGGGTTTGGTCGGTTGTAGAAGTCAAAAACCAAACCTGCAATTTTTT TTATCATTGCAGCAGGATTTGAATTCAATCCTTTTACCAGTGCTGTGCATAACTGCTTTAAAGC AGATAGCTTTTTATCTCTTTCTATGTCCACAAGGATAATCTCAGCCTTAAATCCTTCTATTCCA AGAGAATAAAGGTCATCAGGAGAAGGTATGGTATCAAAATGCTCCTTGAGTCTCTTTTCCGGAA TAATGGAATAAAAACCATTGGGTATTGGACCTGAAAGGGATCCGCTAGACCATAATGTCTGAGC AGCCTGCAATGAATGACCAACTTCCCTAGAATCAAGGGAAGAATATGCAGAATCAAAATTCCTT TCCTGTTTAGTCAGGGGCAGGGACTGGAACTTCTGCTCCAAATGGGAGGGCCAATTCCGGTCTG AAGGGTGTGTCTGGGATCTTCCTTCATCTCCTGGCAGATCATCCATCTCCAAAATATGGTGAAA TAGAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACGTTTAAATGAACAAGGAA ACAGATTGAACATATTATC
Genomic sequence	CTTTGAGCACATAGAGGACTATTTGGTTCAAGAGGAGAATCACAGGAATCATAGTCGGCTGAAT CACTTTCTCCAGTTGCAGACATATGGGATGTGACAACAGCTTTGGATGAAAATGGAACTAGTTG TCCTGGAAAACGCATCAGGTCAACTAGAAACTCCGCAGATTTCAGAATGACCACAACAGACATA TGTTTGGATGAATTATCATATCCATGAGGTTCTTCATTTGGAATGCCCTGCACAAGTTATTGAT GTAGGAAGTAGGATTAGGAAATTCCATTTGAAGAGATGAATACTATTTCATGTTCAGACATACT GATGAAAGGTAAAAAACATACCACCAGCAGTTTAGAATCTATACCAACTGAGTCAGCAAGGACT TTAAATAATATAGCTTTGGGCCTGCAAGATCCATGTCTTATCTGTCCCAGCAATTGAACTCCTC GATTTTCTAATAAATTGGAAAGATCTTCAGAGGATGTTCTTGCAGGACTGAGATGTGGGTTTGG TCGGTTGTAGAAGTCAAAAACCTGAAATTATCATTAAAAATATGAAGTTAAAGAGAAGTAATAC ATACTTAATATGGCATTTTATATAGGTCAAAAGAATGAAAAAATAATCAATGGTTTGGAAAGAC GAAAGATCATTGATACTTCAAGCACCAAGATTACAAATCACCAAATACATGAGCGAAGTAGAAA TGGAACAGTTTCAACTAGGAAAATTCTATTTAAACCATTTTAAGGTAATCAATCACAAGGGTGA ATCTTGCAGCACTCTGAAAAGGGAAAAAGTTAGCATGATCATCCTACATTTTGTAAAGAAGCCC ACGGAAAACTTACCAAACCTGCAATTTTTTTTATCATTGCAGCAGGATTTGAATTCAATCCTTT TACCAGTGCTGTGCATAACTGCTTTAAAGCAGATAGCTTTTTATCTCTTTCTATGTCCACAAGG ATAATCTCAGCCTTAAATCCTTCTATTCCAAGAGAATAAAGGTCATCAGGAGAAGGTATGGTAT CAAAATGCTCCTTGAGTCTCTTTTCCTGCAATGTTCAGAGTCAACAGATGAACTAAAATGCCAA AGCAAGTTACTCATAATCTTTTAACAAGTTAATGTCATTTAAAAAGGCTTCTCATACCGGAATA ATGGAATAAAAACCATTGGGTATTGGACCTGAAAGGGATCCGCTAGACCATAATGTCTGAGCAG CCTGCAATGAATGACCAACTTCCCTAGAATCAAGGGAAGAATATGCAGAATCAAAATTCCTTTC CTGTTTAGTCAGGGGCAGGGACTGGAACTTCTGCTCCAAATGGGAGGGCCAATTCCGGTCTGAA GGGTGTGTCTGGGATCTTCCTTCATCTCCTGGCAGATCATCCATCTCCAAAATATGGTGAAATA GAGAATCATTTTGCTTCAATTATCATCCTTCAAGGCCACTCTACGTTTAAATGAACAAGGAAAC AGATTGAACATATTATC

			
						 Conservation Information
					
						Conserved circRNAs
						
							NA						
					
						PMCS
						0.136138649

Conservation Information
Conserved circRNAs	NA
PMCS	0.136138649

			
						 Functional Information
					
						Coding potential
						Y
					
						Potential coding position
						
							232718000-232719412(-)
232719376-232719426(-)
						
						Potential amino acid sequence
						
							MCSKDNMFNLFPCSFKRRVALKDDN*(-)
MDDLPGDEGRSQTHPSDRNWPSHLEQKFQSLPLTKQERNFDSAYSSLDSREVGHSLQAAQTLWS
SGSLSGPIPNGFYSIIPEKRLKEHFDTIPSPDDLYSLGIEGFKAEIILVDIERDKKLSALKQLC
TALVKGLNSNPAAMIKKIAGLVFDFYNRPNPHLSPARTSSEDLSNLLENRGVQLLGQIRHGSCR
PKAILFKVLADSVGIDSKLLVGIPNEEPHGYDNSSKHMSVVVILKSAEFLVDLMRFPGQLVPFS
SKAVVTSHMSATGESDSADYDSCDSPLEPNSPLCAQRIICSICFLVHLNVEWP*(-)
						
						Sponge-miRNAs
						
							NA						
					
						circRNA-miRNA-mRNA network
						 VISUALIZATION
					
						Potential function description
						responsive to drought stress

Functional Information
Coding potential	Y
Potential coding position	232718000-232719412(-) 232719376-232719426(-)
Potential amino acid sequence	MCSKDNMFNLFPCSFKRRVALKDDN(-) MDDLPGDEGRSQTHPSDRNWPSHLEQKFQSLPLTKQERNFDSAYSSLDSREVGHSLQAAQTLWS SGSLSGPIPNGFYSIIPEKRLKEHFDTIPSPDDLYSLGIEGFKAEIILVDIERDKKLSALKQLC TALVKGLNSNPAAMIKKIAGLVFDFYNRPNPHLSPARTSSEDLSNLLENRGVQLLGQIRHGSCR PKAILFKVLADSVGIDSKLLVGIPNEEPHGYDNSSKHMSVVVILKSAEFLVDLMRFPGQLVPFS SKAVVTSHMSATGESDSADYDSCDSPLEPNSPLCAQRIICSICFLVHLNVEWP(-)
Sponge-miRNAs	NA
circRNA-miRNA-mRNA network	VISUALIZATION
Potential function description	responsive to drought stress

			
						 Other Information
					
						References
						Ma et al., 2021b;Zhang et al., 2019

circRNA

Detail information of Zm00001d053515_circ_g.4

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